project: _E. coli_ promoter transcription initiation model project
In lptolik/R4Kappa: Kappa simulation Project

Description Usage Format Examples

The project is build around E. coli promoter transcription initiation model. The purpose of the project is to compare sensitivity of parameters of the model in parallel and concurrent regimes.

1	data(project)

The format is: List of 13 $ name : chr "lot.of.dna1" $ date : chr "20120607181510" $ constLines :List of 3 ..$ main_rnap_def_rule.ka: chr [1:27] "#basic promoter part description" " ..$ main_rnap_init.ka : chr [1:3] " ..$ main_rnap_param.ka : chr [1:7] " $ templateLines:List of 3 ..$ var_prom_def.ka : chr [1:15] "#variable promoter part description" " ..$ var_prom_init.ka: chr [1:2] " ..$ var_prom_rule.ka: chr [1:23] "#var_prom_rule.ka" "'promoter_- nonspec' RNAP (dna,st~f),promoter_- (ns,s35,s10~f)-> RNAP (dna!1,st~n),promoter_- (ns!1,s35,s10~f) @ ('kns'*'pns_-'"| __truncated__ "'prom_- ns diss' RNAP (dna!1,st~n),promoter_- (ns!1,s35,s10~f) -> RNAP (dna,st~f),promoter_- (ns,s35,s10~f) @ ('k_ns'*'p_ns_-')"| __truncated__ "'recognitionUp_-' RNAP (sigmaS!_,dna!1,st~n,alpha),promoter_- (ns!1,up) -> RNAP (sigmaS!_,dna!1,st~pr,alpha!2),promoter_- (ns!"| __truncated__ ... $ replaceRegexp: chr "_-" $ nRep : num 10 $ nSets : num 500 $ execPath : chr "/exports/home/osorokin/kasim3/KaSim" $ type : chr "both" $ shLines :List of 3 ..$ run.sh.templ: chr [1:22] "#!/bin/bash" "numEv=10" "time=1000" "if [ \"$1\" != \"\" ]; then" ... ..$ jobConc.sh : chr [1:21] "#!/bin/bash" "########################################" "# #" "# SGE MPI job script for ECDF Cluster #" ... ..$ job.sh.templ: chr [1:21] "#!/bin/bash" "########################################" "# #" "# SGE MPI job script for ECDF Cluster #" ... $ paramLines :List of 1 ..$ var_prom_param.ka: chr [1:19] "#var_prom_param.ka" " $ pTable :'data.frame': 18 obs. of 5 variables: ..$ i : num [1:18] 1 2 3 4 5 6 7 8 9 10 ... ..$ name: chr [1:18] "p_ns_-" "pns_-" "k35_-" "kb10_-" ... ..$ str : num [1:18] 2 3 4 5 6 7 8 9 10 11 ... ..$ min : num [1:18] 0.01 0.0001 0 0 1.7 0.67 0.05 3.6 0.14 0.35 ... ..$ max : num [1:18] 10000 100 0 0 170 67 5 360 14 35 ... $ paramSets :'data.frame': 500 obs. of 18 variables: ..$ p_ns : num [1:500] 2912 1153 9848 7942 1672 ... ..$ pns : num [1:500] 27.2 77.9 23.2 88.4 12 ... ..$ k35 : num [1:500] 0 0 0 0 0 0 0 0 0 0 ... ..$ kb10 : num [1:500] 0 0 0 0 0 0 0 0 0 0 ... ..$ k_35 : num [1:500] 169 100.9 30.9 140.3 70.4 ... ..$ k_10 : num [1:500] 42.61 29.55 62.98 4.86 37.78 ... ..$ kb_10 : num [1:500] 2.305 0.469 4.99 0.938 3.913 ... ..$ k35i : num [1:500] 220 113 292 352 176 ... ..$ kb10i : num [1:500] 6.55 3.42 8.81 11.41 4.29 ... ..$ k10 : num [1:500] 10.52 18.09 4.42 16.42 32.26 ... ..$ kelong : num [1:500] 0.763 0.22 0.615 0.37 0.964 ... ..$ ksynt : num [1:500] 93.9 19.3 105.4 40.3 127.7 ... ..$ kuntouch: num [1:500] 225 165 290 129 338 ... ..$ kUP : num [1:500] 177.8 127 68.6 190.4 40.7 ... ..$ k_UP : num [1:500] 32.1 275.4 138.8 188 51.1 ... ..$ kreset : num [1:500] 9.16e-04 3.60e-04 1.19e-03 1.46e-03 6.89e-05 ... ..$ kinit : num [1:500] 1.461 3.348 0.448 1.976 2.803 ... ..$ ksigma : num [1:500] 2.487 1.585 0.145 0.743 2.183 ... - attr(*, "class")= chr "kproject"